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Results for “chain conformation”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

De Novo Design of Molecular Recognition for Sequence Defined Polymers

The proposed research aims at developing a computational framework that allows the de novo design of sequence defined polymers for molecular recognition. This framework will include the prediction of the 1) accessible backbone conformational space in solution environments for small to medium polymer length and 2) how side chains of different size and functionality can be used to design convergent or divergent receptor configurations. A structural database inspired by the protein database will be build that can be used to construct larger scaffolds based on smaller sequences

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

The Influence of Alkyl Spacers and Molecular Weight on the Charge Transport and Storage Properties of Oxy‐Bithiophene‐Based Conjugated Polymers

Abstract Conjugated polymers (CPs) with polar side chains can conduct electronic and ionic charges simultaneously, making them promising for bioelectronics, electrocatalysis and energy storage. Recent work showed that adding alkyl spacers between CP backbones and polar side chains improved electronic charge carrier mobility, reduced swelling and enhanced stability, without compromising ion transport. However, how alkyl spacers impact polymer backbone conformation and, subsequently, electronic properties remain unclear. In this work, we design two oxy‐bithiophene‐based CP series, each featuring progressively extended alkyl spacer lengths and two distinct molecular weight (MW) distributions. Using operando characterisations, we evaluate the (spectro)electrochemical and swelling properties of the polymer thin films, and their performance in organic field‐effect transistors and organic electrochemical transistors. Surprisingly, alkyl spacers negatively impact the hole mobility of our polymers, with higher MW amplifying this effect. Using molecular dynamics simulations, we show that it is thermodynamically favourable for adjacent non‐polar alkyl spacers to aggregate in polar electrolytes, leading to backbone twisting. Further spectroscopic measurements corroborate this prediction. Our findings demonstrate the active interactions between side chain structure, MW and electrolyte/solvent polarity in influencing polymer performance, underscoring the importance of considering solvation environment effects on polymer conformation when designing new mixed conducting CPs for electrochemical applications.

Yu, Hang [Department of Physics and Centre for Pro↗
DOE OSTI2024

The Influence of Alkyl Spacers and Molecular Weight on the Charge Transport and Storage Properties of Oxy‐Bithiophene‐Based Conjugated Polymers

Conjugated polymers (CPs) with polar side chains can conduct electronic and ionic charges simultaneously, making them promising for bioelectronics, electrocatalysis and energy storage. Recent work showed that adding alkyl spacers between CP backbones and polar side chains improved electronic charge carrier mobility, reduced swelling and enhanced stability, without compromising ion transport. However, how alkyl spacers impact polymer backbone conformation and, subsequently, electronic properties remain unclear. In this work, we design two oxy-bithiophene-based CP series, each featuring progressively extended alkyl spacer lengths and two distinct molecular weight (MW) distributions. Using operando characterisations, we evaluate the (spectro)electrochemical and swelling properties of the polymer thin films, and their performance in organic field-effect transistors and organic electrochemical transistors. Surprisingly, alkyl spacers negatively impact the hole mobility of our polymers, with higher MW amplifying this effect. Using molecular dynamics simulations, we show that it is thermodynamically favourable for adjacent non-polar alkyl spacers to aggregate in polar electrolytes, leading to backbone twisting. Further spectroscopic measurements corroborate this prediction. Our findings demonstrate the active interactions between side chain structure, MW and electrolyte/solvent polarity in influencing polymer performance, underscoring the importance of considering solvation environment effects on polymer conformation when designing new mixed conducting CPs for electrochemical applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Local conformations and heterogeneities in structures and dynamics of isotactic polypropylene adsorbed onto carbon fiber

Carbon fiber (CF) reinforced polymers (CFRPs) have experienced widespread use in various industries. One of the most important parameters that controls the macroscopic property of CFRPs is the interface between a polymer matrix and CF. There is growing evidence to suggest the formation of a bound polymer layer (BPL), i.e., polymer chains that physically adsorb on a filler surface. However, this interface is always in contact with the thicker part of a polymer matrix, rendering its understanding a difficult task. Therein, we use CF-reinforced isotactic polypropylene (iPP) as a rational CFRP. To characterize the BPL on the CF surface, we extracted it from the CFRP using solvent-rinsing with p-xylene. The physical and thermal properties of the BPL were characterized by differential scanning calorimetry and thermogravimetric analysis, while its microscopic structures and dynamics were probed by small-angle neutron scattering and quasi-elastic neutron scattering (QENS) techniques. Subsequently, we employed atomistic molecular dynamics (MD) simulations to complement the QENS results above the bulk melting temperature and reveal details that were experimentally inaccessible. In this work, we observed that the degree of crystallinity of the BPL was quite lower than the bulk, while the melting temperature of the BPL remained the same as the bulks. Within the given length and time scales probed by QENS and MD, we also observed that most of the bound chains were mobile, with the formation of a high-density region (less than 1 nm in thickness) near the CF surface. The segmental dynamics of the bound chains probed by both QENS and MD were also much faster than those of the free chains, possibly due to the presence of a free surface region at the topmost surface of the BPL. Furthermore, the MD results demonstrated that the backbone chains and side groups lie nearly flat on the CF surface, which is the driving force for the flattening process of the iPP BPL to overcome the conformational entropy loss in the total free energy.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Structural basis for Ca2+-dependent activation of a plant metacaspase

Abstract Plant metacaspases mediate programmed cell death in development, biotic and abiotic stresses, damage-induced immune response, and resistance to pathogen attack. Most metacaspases require Ca 2+ for their activation and substrate processing. However, the Ca 2+ -dependent activation mechanism remains elusive. Here we report the crystal structures of Metacaspase 4 from Arabidopsis thaliana ( At MC4) that modulates Ca 2+ -dependent, damage-induced plant immune defense. The At MC4 structure exhibits an inhibitory conformation in which a large linker domain blocks activation and substrate access. In addition, the side chain of Lys225 in the linker domain blocks the active site by sitting directly between two catalytic residues. We show that the activation of At MC4 and cleavage of its physiological substrate involve multiple cleavages in the linker domain upon activation by Ca 2+ . Our analysis provides insight into the Ca 2+ -dependent activation of At MC4 and lays the basis for tuning its activity in response to stresses for engineering of more sustainable crops for food and biofuels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Selective inhibition of human translation termination by a drug-like compound

Methods to directly inhibit gene expression using small molecules hold promise for the development of new therapeutics targeting proteins that have evaded previous attempts at drug discovery. Among these, small molecules including the drug-like compound PF-06446846 (PF846) selectively inhibit the synthesis of specific proteins, by stalling translation elongation. These molecules also inhibit translation termination by an unknown mechanism. Using cryo-electron microscopy (cryo-EM) and biochemical approaches, we show that PF846 inhibits translation termination by arresting the nascent chain (NC) in the ribosome exit tunnel. The arrested NC adopts a compact α-helical conformation that induces 28 S rRNA nucleotide rearrangements that suppress the peptidyl transferase center (PTC) catalytic activity stimulated by eukaryotic release factor 1 (eRF1). These data support a mechanism of action for a small molecule targeting translation that suppresses peptidyl-tRNA hydrolysis promoted by eRF1, revealing principles of eukaryotic translation termination and laying the foundation for new therapeutic strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Craspase is a CRISPR RNA-guided, RNA-activated protease

The CRISPR-Cas type III-E RNA-targeting effector complex gRAMP/Cas7-11 is associated with a caspase-like protein (TPR-CHAT/Csx29) to form Craspase (CRISPR-guided caspase). Here, we use cryo–electron microscopy snapshots of Craspase to explain its target RNA cleavage and protease activation mechanisms. Target-guide pairing extending into the 5' region of the guide RNA displaces a gating loop in gRAMP, which triggers an extensive conformational relay that allosterically aligns the protease catalytic dyad and opens an amino acid side-chain–binding pocket. We further define Csx30 as the endogenous protein substrate that is site-specifically proteolyzed by RNA-activated Craspase. This protease activity is switched off by target RNA cleavage by gRAMP and is not activated by RNA targets containing a matching protospacer flanking sequence. We thus conclude that Craspase is a target RNA–activated protease with self-regulatory capacity.

Science & Technology - Other Topics↗
DOE OSTI2025

Shear-Induced Conformations of Salt-Free Polyelectrolytes in Semidilute Solutions

Here, we present coarse-grained molecular dynamics simulations of salt-free polyelectrolyte chains in semidilute solutions under simple shear flow, with full hydrodynamic interactions and explicit dipolar solvent. At equilibrium, chain orientation statistics follow a pseudo-Voigt distribution, and the structural correlation length and chain end-to-end vector autocorrelation function exhibit scaling behavior consistent with theoretical predictions for polyelectrolytes. Under shear, chains transition from coiled to stretched states and the end-to-end vector autocorrelation function reveals oscillatory dynamics at high Weissenberg numbers. Analysis of the gyration tensor and shear strain distributions identified three distinct chain populations with directional alignment along and against the shear gradient. Compared with their neutral polymer counterparts, polyelectrolytes exhibit stronger shear thinning and enhanced chain alignment under the same Weissenberg number, which is attributed to electrostatic interactions and shear-induced counterion release. These findings provide molecular insight into the distinct flow response of charged polymers and have implications for tailoring the rheological properties of polyelectrolyte-based materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Conformational motions and ligand-binding underlying gating and regulation in IP 3 R channel

Inositol-1,4,5-trisphosphate receptors (IP3Rs) are activated by IP 3 and Ca 2+ and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single particle cryo-EM analysis we determined 3D structures of the nanodisc-reconstituted IP 3 R1 channel in two ligand-bound states. These structures provide unprecedented details governing binding of IP 3 , Ca 2+ and ATP, revealing conformational changes that couple ligand-binding to channel opening. Using a deep-learning approach and 3D variability analysis we extracted molecular motions of the key protein domains from cryo-EM density data. We find that IP 3 binding relies upon intrinsic flexibility of the ARM2 domain in the tetrameric channel. Our results highlight a key role of dynamic side chains in regulating gating behavior of IP 3 R channels. This work represents a stepping-stone to developing mechanistic understanding of conformational pathways underlying ligand-binding, activation and regulation of the channel.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Improving the bioaccessibility of lipophilic ingredient in its oral intestinal delivery by ultrasound and biological cross‐linker

Abstract BACKGROUND Great efforts have been made to improve the oral bioaccessibility of lipophilic ingredients with multi‐functionalities. Achieving intestinal delivery of lipophilic ingredients and their encapsulation in micelles composed of bile salts and lipid hydrolysates (i.e. fatty acids) is critical for improving oral bioaccessibility. Therefore, oil‐core microcapsules are considered ideal carriers of lipophilic ingredients. Previous studies have reported oil‐core/zein‐shell microcapsules constructed by a one‐step anti‐solvent process. Still, its efficacy as an intestinal delivery system was limited because if the porous shell structure. RESULTS Zein solution was pretreated with ultrasound and tannic acid (TA) cross‐linking. Composite oil‐core microcapsule (COM) with a compact shell structure was successfully prepared by using modified zein solution in the anti‐solvent process. Fourier‐transform infrared spectroscopy and circular dichroism analyses indicated that ultrasound and TA synergistically promote the conformational transition of zein from α‐helix to β‐sheet and enhance the hydrophobic interactions among protein chains. The above changes contribute to the strengthen of shell zein network. Correspondingly, COM presents superior encapsulation efficiency and environmental stability over the simple oil‐core microcapsule (SOM) prepared without the use of ultrasound and TA. Furthermore, antioxidant activity of β‐carotene was well retained during the encapsulation process. In vitro studies indicated that COM was more resistant to digestibility and acid‐induced swelling. More than 87% of β‐carotene could be released in the intestine in a sustainable way. The controllable release behavior thus promoted a significant increase in bioaccessibility of β‐carotene encapsulated in COM compared to SOM (85.9% versus 48.5%). CONCLUSION The COM generated here shows potential for bioaccessibility improvement of lipophilic ingredients. © 2022 Society of Chemical Industry.

Wei, Yun‐Shan↗
DOE OSTI2023

Properties of Gaseous Deprotonated L-Cysteine S-Sulfate Anion [cysS-SO3]−: Intramolecular H-Bond Network, Electron Affinity, Chemically Active Site, and Vibrational Fingerprints

L-cysteine S-sulfate, Cys-SSO3H, and their derivatives play essential roles in biological chemistry and pharmaceutical synthesis, yet their intrinsic molecular properties have not been studied to date. In this contribution, the deprotonated anion [cysS-SO3]− was introduced in the gas phase by electrospray and characterized by size-selected, cryogenic, negative ion photoelectron spectroscopy. The electron affinity of the [cysS-SO3]• radical was determined to be 4.95 ± 0.10 eV. In combination with theoretical calculations, it was found that the most stable structure of [cysS-SO3]− (S1) is stabilized via three intramolecular hydrogen bonds (HBs); i.e., one O-H……N between the -COOH and -NH2 groups, and two N-H……O HBs between -NH2 and -SO3, in which the amino group serves as both HB acceptor and donor. In addition, a nearly iso-energetic conformer (S2) with the formation of an O-H……N-H……O-S chain-type binding motif competes with S1 in the source. The most reactive site of the molecule susceptible for electrophilic attacks is the linkage S atom. Theoretically predicted infrared spectra indicate that O-H and N-H stretching modes are the fingerprint region (2800 to 3600 cm−1) to distinguish different isomers. The obtained information lays out a foundation to better understand the transformation and structure–reactivity correlation of Cys-SSO3H in biologic settings.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Effect of Crystallinity on Polymer Chain Compression in Polyethylene Dynamically Loaded with In-Situ X-Ray Diffraction

Abstract Polyethylene (PE) is a polymer widely used in commercial applications, where the properties of PE can be altered based on the molecular conformation. In this study, shock compression experiments with in-situ x-ray diffraction were conducted on two conformations of PE– low density polyethylene (LDPE) and ultra-high molecular weight polyethylene (UHMWPE). Encouragingly, X-ray diffraction patterns were easily observed in LDPE, which is only 25% crystalline. In agreement with a previous study on HDPE, LDPE exhibited a phase transition at 7.7 GPa. Lower pressure experiments on UHMWPE and LDPE exhibited polymer chain compression, but no occurrence of a phase transition.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Simulation studies of polypeptoids using replica exchange with dynamical scaling and dihedral biasing

Polypeptoids differ from polypeptides in that the amide bond can more frequently adopt both cis and trans conformations. The transition between the two conformations requires overcoming a large energy barrier, making it difficult for conventional molecular simulations to adequately visit the cis and trans structures. A replica-exchange method is presented that allows for easy rotations of the amide bond and also an efficient linking to a high temperature replica. The method allows for just three replicas (one at the temperature and Hamiltonian of interest, a second high temperature replica with a biased dihedral potential, and a third connecting them) to overcome the amide bond sampling problem and also enhance sampling for other coordinates. Here our results indicate that for short peptoid oligomers, the conformations can range from all cis to all trans with an average cis/trans ratio that depends on side chain and potential model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Crystal structure of vancomycin bound to the resistance determinant D -alanine- D -serine

Vancomycin is a glycopeptide antibiotic that for decades has been a mainstay of treatment for persistent bacterial infections. However, the spread of antibiotic resistance threatens its continued utility. In particular, vancomycin-resistant enterococci (VRE) have become a pressing clinical challenge. Vancomycin acts by binding and sequestering the intermediate Lipid II in cell-wall biosynthesis, specifically recognizing a D-alanine-D-alanine dipeptide motif within the Lipid II molecule. VRE achieve resistance by remodeling this motif to either D-alanine-D-lactate or D-alanine-D-serine; the former substitution essentially abolishes recognition by vancomycin of Lipid II, whereas the latter reduces the affinity of the antibiotic by roughly one order of magnitude. The complex of vancomycin bound to D-alanine-D-serine has been crystallized, and its 1.20 Å X-ray crystal structure is presented here. This structure reveals that the D-alanine-D-serine ligand is bound in essentially the same position and same pose as the native D-alanine-D-alanine ligand. The serine-containing ligand appears to be slightly too large to be comfortably accommodated in this way, suggesting one possible contribution to the reduced binding affinity. In addition, two flexible hydroxyl groups – one from the serine side chain of the ligand, and the other from a glucose sugar on the antibiotic – are locked into single conformations in the complex, which is likely to contribute an unfavorable entropic component to the recognition of the serine-containing ligand.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Probing Interactions between Adsorbed Polymers and γ-Al 2 O 3 Using Solid-State NMR

The interactions between polymers and metal oxide surfaces affect the physical properties of polymer composites and the selectivity of catalysts used for plastic conversion. Gauging the strengths of these interactions and how they depend on adsorption conformations and polymer structure is nevertheless quite challenging. Herein, we evaluate whether a recently introduced dynamic nuclear polarization-based surface-to-atom distance measurement method can be used to gauge the specific interactions between five vinyl polymers and an oxide support (alumina). The adsorption conformations of polymer monolayers were studied using site-specific 13 C{ 27 Al} rotational-echo saturation-pulse double-resonance (RESPDOR) experiments. The method is effective in revealing the average distance between the adsorbed polymer and the surface, as well as the fraction of the monomers that are adsorbed. Polymers that possess larger side chains are more weakly adsorbed, as evidenced by their formation of more numerous loop and tail structures. In conclusion, the measured RESPDOR dephasing data further reveals that polymer adsorption conformations are largely disordered and involve few hydrogen bonding interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Understanding the Origin of Structural Diversity of DNA Double Helix

Deciphering the contribution of DNA subunits to the variability of its 3D structure represents an important step toward the elucidation of DNA functions at the atomic level. In the pursuit of that goal, our previous studies revealed that the essential conformational characteristics of the most populated “canonic” BI and AI conformational families of Watson–Crick duplexes, including the sequence dependence of their 3D structure, preexist in the local energy minima of the elemental single-chain fragments, deoxydinucleoside monophosphates (dDMPs). Those computations have uncovered important sequence-dependent regularity in the superposition of neighbor bases. The present work expands our studies to new minimal fragments of DNA with Watson–Crick nucleoside pairs that differ from canonic families in the torsion angles of the sugar-phosphate backbone (SPB). To address this objective, computations have been performed on dDMPs, cdDMPs (complementary dDMPs), and minimal fragments of SPBs of respective systems by using methods of molecular and quantum mechanics. These computations reveal that the conformations of dDMPs and cdDMPs having torsion angles of SPB corresponding to the local energy minima of separate minimal units of SPB exhibit sequence-dependent characteristics representative of canonic families. In contrast, conformations of dDMP and cdDMP with SPB torsions being far from the local minima of separate SPB units exhibit more complex sequence dependence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Solid‐Adsorbed Polymer‐Electrolyte Interphases for Stabilizing Metal Anodes in Aqueous Zn and Non‐Aqueous Li Batteries

Abstract Polymers are known to adsorb spontaneously from liquid solutions in contact with high‐energy substrates to form configurationally complex, but robust phases that often exhibit higher durability than might be expected from the individual physical bonds formed with the substrate. Rational control of the physical, chemical, and transport properties of such interphases has emerged as a fundamental opportunity for scientific and technological advances in energy storage technology but requires in‐depth understanding of the conformation states and electrochemical effect of the adsorbed polymers. Here, we analyze the interfacial adsorption of oligomeric polyethylene glycol (PEG) chains of moderate sizes dissolved in protic and aprotic liquid electrolytes and find that there is an optimum polymer molecular weight of approximately 400 Da at which the highest columbic efficiency is achieved for both Zn and Li deposition. These findings point to a simple, versatile approach for extending the lifetime of batteries.

Jin, Shuo↗
DOE OSTI2023

Solid–Adsorbed Polymer–Electrolyte Interphases for Stabilizing Metal Anodes in Aqueous Zn and Non–Aqueous Li Batteries

Polymers are known to adsorb spontaneously from liquid solutions in contact with high-energy substrates to form configurationally complex, but robust phases that often exhibit higher durability than might be expected from the individual physical bonds formed with the substrate. Rational control of the physical, chemical, and transport properties of such interphases has emerged as a fundamental opportunity for scientific and technological advances in energy storage technology but requires in-depth understanding of the conformation states and electrochemical effect of the adsorbed polymers. Here, we analyze the interfacial adsorption of oligomeric polyethylene glycol (PEG) chains of moderate sizes dissolved in protic and aprotic liquid electrolytes and find that there is an optimum polymer molecular weight of approximately 400 Da at which the highest columbic efficiency is achieved for both Zn and Li deposition. Furthermore, these findings point to a simple, versatile approach for extending the lifetime of batteries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗